GapMind for catabolism of small carbon sources


D-glucose-6-phosphate catabolism

Analysis of pathway glucose-6-P in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 uhpT
Azospirillum brasilense Sp245 uhpT
Bacteroides thetaiotaomicron VPI-5482 uhpT
Burkholderia phytofirmans PsJN uhpT
Caulobacter crescentus NA1000 uhpT
Cupriavidus basilensis 4G11 uhpT
Dechlorosoma suillum PS uhpT
Desulfovibrio vulgaris Hildenborough uhpT
Desulfovibrio vulgaris Miyazaki F uhpT
Dinoroseobacter shibae DFL-12 uhpT
Dyella japonica UNC79MFTsu3.2 uhpT
Echinicola vietnamensis KMM 6221, DSM 17526 uhpT
Escherichia coli BW25113 uhpT
Herbaspirillum seropedicae SmR1 uhpT
Klebsiella michiganensis M5al uhpT
Magnetospirillum magneticum AMB-1 uhpT
Marinobacter adhaerens HP15 uhpT
Paraburkholderia bryophila 376MFSha3.1 uhpT
Pedobacter sp. GW460-11-11-14-LB5 uhpT
Phaeobacter inhibens BS107 uhpT
Pseudomonas fluorescens FW300-N1B4 uhpT
Pseudomonas fluorescens FW300-N2C3 uhpT
Pseudomonas fluorescens FW300-N2E2 uhpT
Pseudomonas fluorescens FW300-N2E3 uhpT
Pseudomonas fluorescens GW456-L13 uhpT
Pseudomonas putida KT2440 uhpT
Pseudomonas simiae WCS417 uhpT
Pseudomonas stutzeri RCH2 uhpT
Shewanella amazonensis SB2B uhpT
Shewanella loihica PV-4 uhpT
Shewanella oneidensis MR-1 uhpT
Shewanella sp. ANA-3 uhpT
Sinorhizobium meliloti 1021 uhpT
Sphingomonas koreensis DSMZ 15582 uhpT
Synechococcus elongatus PCC 7942 uhpT

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory